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At least 847 records · Page 47

Low-level resource partitioning supports coexistence among functionally redundant bacteria during successional dynamics

Members of microbial communities can substantially overlap in substrate use. However, what enables functionally redundant microorganisms to coassemble or even stably coexist remains poorly understood. Here, we show that during unstable successional dynamics on complex, natural organic matter, functionally redundant bacteria can coexist by partitioning low-concentration substrates even though they compete for one simple, dominant substrate. We allowed ocean microbial communities to self-assemble on leachates of the brown seaweed Fucus vesiculosus and then analyzed the competition among 10 taxonomically diverse isolates representing two distinct stages of the succession. All, but two isolates, exhibited an average of 90% ± 6% pairwise overlap in resource use, and functional redundancy of isolates from the same assembly stage was higher than that from between assembly stages, leading us to construct a simpler four-isolate community with two isolates from each of the early and late stages. We found that, although the short-term dynamics of the four-isolate communities in F. vesiculosus leachate was dependent on initial isolate ratios, in the long term, the four isolates stably coexist in F. vesiculosus leachate, albeit with some strains at low abundance. We therefore explored the potential for nonredundant substrate use by genomic content analysis and RNA expression patterns. This analysis revealed that the four isolates mainly differed in peripheral metabolic pathways, such as the ability to degrade pyrimidine, leucine, and tyrosine, as well as aromatic substrates. These results highlight the importance of fine-scale differences in metabolic strategies for supporting the frequently observed coexistence of large numbers of rare organisms in natural microbiomes.

59 BASIC BIOLOGICAL SCIENCES↗

Unified wavefront singularity characterization of three-dimensional elastodynamic time-domain half-space Green's function under impulsive boundary and internal loads

Founded on a novel analytical formulation that led to a rigorous yet compact path-integral representation of the time-domain elastodynamic half-space Green's function, a unified analysis of the possible occurrence of different singular wavefront behaviour in the response under arbitrary impulsive internal or surface point loads at arbitrary source-receiver locations is presented. With the decomposition of the general solution into distinct initiating and reflected wave group integrals that share a common factored format and simple contour definitions, the mathematical framework is shown to allow a straightforward identification of the specific conditions and the particular wave groups that are responsible for the singular wavefront phenomena without resorting to advanced analytic function theories or asymptotic methods. Analytic characterizations of the nature, strength and direction of all intrinsic singular wavefront behaviours of the three-dimensional Green's function in three canonical cases of source-receiver configurations are given in a dual integral-closed form format to facilitate their theoretical understanding as well as computational applications. Graphical illustrations of their variation with the source-receiver configuration and the medium's Poisson's ratio together with relevant comparison and clarifications of some classical treatments are included.

Green’s functions↗

Numerically exact generalized Green's function cluster expansions for electron-phonon problems

We generalize the family of approximate momentum average methods to formulate a numerically exact, convergent hierarchy of equations whose solution provides an efficient algorithm to compute the Green's function of a particle dressed by bosons suitable in the entire parameter regime. We use this approach to extract ground-state properties and spectral functions. Our approximation-free framework, dubbed the generalized Green's function cluster expansion (GGCE), allows access to exact numerical results in the extreme adiabatic limit, where many standard methods struggle or completely fail. We showcase the performance of the method, specializing three important models of charge-boson coupling in solids and molecular complexes: the molecular Holstein model, which describes coupling between charge density and local distortions, the Peierls model, which describes modulation of charge hopping due to intersite distortions, and a more complex Holstein + Peierls system with couplings to two different phonon modes, paradigmatic of charge-lattice interactions in organic crystals. Furthermore, the GGCE serves as an efficient approach that can be systematically extended to different physical scenarios, thus providing a tool to model the frequency dependence of dressed particles in realistic settings.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Calculating the hyperfine tensors for group-IV impurity-vacancy centers in diamond using hybrid density functional theory

The hyperfine interaction is an important probe for understanding the structure and symmetry of defects in a semiconductor. Density functional theory has shown that it can provide useful first-principles predictions for both the hyperfine tensor and the hyperfine constants that arise from it. Recently there has been great interest in using group-IV impurity-vacancy color centers XV – (where X = Si, Ge, Sn, or Pb and V is a carbon vacancy) for important applications in quantum computing and quantum information science. In this paper we have calculated the hyperfine tensors for these XV – color centers using the HSE06 screened Hartree-Fock hybrid exchange-correlation functional with the inclusion of core electron spin polarization. We have compared our results to calculations which only use the PBE exchange-correlation functional without the inclusion of core electron spin polarization and we have found that our results are in very good agreement with available experimental results. Lastly, we have theoretically shown that these XV – color centers exhibit a Jahn-Teller distortion which explains the observed anisotropic distribution of the hyperfine constants among the neighboring 13 C nuclear spins.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Fast and robust all-electron density functional theory calculations in solids using orthogonalized enriched finite elements

Here, we present a computationally efficient approach to perform systematically convergent real-space all-electron Kohn-Sham density functional theory calculations for solids using an enriched finite element (FE) basis. The enriched FE basis is constructed by augmenting the classical FE basis with atom-centered numerical basis functions, comprising of atomic solutions to the Kohn-Sham problem. Notably, to improve the conditioning, we orthogonalize the enrichment functions with respect to the classical FE basis, without sacrificing the locality of the resultant basis. In addition to improved conditioning, this orthogonalization procedure also renders the overlap matrix block diagonal, greatly simplifying its inversion. Subsequently, we use a Chebyshev polynomial based filtering technique to efficiently compute the occupied eigenspace in each self-consistent field iteration. We demonstrate the accuracy and efficiency of the proposed approach on periodic unit cells and supercells. The benchmark studies show a staggering 130× speedup of the orthogonalized enriched FE basis over the classical FE basis. We also present a comparison of the orthogonalized enriched FE basis with the linearized augmented plane-wave + local orbitals basis, both in terms of accuracy and efficiency. Notably, we demonstrate that the orthogonalized enriched FE basis can handle large system sizes of ~10 000 electrons. Finally, we observe good parallel scalability of our implementation with 92% efficiency at 22× speedup for a system with 620 electrons

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Robust analytic continuation of Green's functions via projection, pole estimation, and semidefinite relaxation

Green's functions of fermions are described by matrix-valued Herglotz-Nevanlinna functions. Since analytic continuation is fundamentally an ill-posed problem, the causal space described by the matrix-valued Herglotz-Nevanlinna structure can be instrumental in improving the accuracy and in enhancing the robustness with respect to noise. We demonstrate a three-pronged procedure for robust analytic continuation called PES: (1) projection of data to the causal space; (2) estimation of pole locations; and (3) semidefinite relaxation within the causal space. We compare the performance of PES with the recently developed Nevanlinna and Carathéodory continuation methods and find that PES is more robust in the presence of noise and does not require the usage of extended precision arithmetics. We also demonstrate that a causal projection improves the performance of the Nevanlinna and Carathéodory methods. The PES method is generalized to bosonic response functions, for which the Nevanlinna and Carathéodory continuation methods have not yet been developed. Furthermore, it is particularly useful for studying spectra with sharp features, as they occur in the study of molecules and band structures in solids.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Covariant density functional theory input for r-process simulations in actinides and superheavy nuclei: The ground state and fission properties

A systematic investigation of the ground-state and fission properties of even-even actinides and superheavy nuclei with Z = 90–120 from the two-proton up to two-neutron drip lines with proper assessment of systematic theoretical uncertainties has been performed for the first time in the framework of covariant density functional theory (CDFT). Furthermore, these results provide a necessary theoretical input for the r-process modeling in heavy nuclei and, in particular, for the study of fission cycling. Four state-of-the-art globally tested covariant energy density functionals (CEDFs), namely, DD-PC1, DD-ME2, NL3*, and PC-PK1, representing the major classes of the CDFT models are employed in the present paper. Ground-state deformations, binding energies, two-neutron separation energies, α-decay Q α values and half-lives, and the heights of fission barriers have been calculated for all these nuclei. Theoretical uncertainties in these physical observables and their evolution as a function of proton and neutron numbers have been quantified and their major sources have been identified. Spherical shell closures at Z = 120, N = 184, and N = 258 and the structure of the single-particle (especially, high-j) states in their vicinities as well as nuclear matter properties of employed CEDFs are two major factors contributing to theoretical uncertainties. However, different physical observables are affected in a different way by these two factors. For example, theoretical uncertainties in calculated ground-state deformations are affected mostly by the former factor, while theoretical uncertainties in fission barriers depend on both of these factors.

190 ≤ A ≤ 219↗

Anchor-based optimization of energy density functionals

A new anchor-based optimization method of defining energy density functionals (EDFs) is proposed. In this approach, the optimization of the parameters of EDFs is carried out for a selected set of spherical anchor nuclei, the physical observables of which are modified by the correction function, which takes into account the global performance of EDFs. It is shown that the use of this approach leads to a substantial improvement in the global description of binding energies for several classes of covariant EDFs. Here, the computational cost of defining a new functional within this approach is drastically lower as compared with the one for the optimization which includes the global experimental data on spherical, transitional, and deformed nuclei in the fitting protocol.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Impact of tensor couplings with scalar mixing on covariant energy density functionals

The recent pioneering campaigns conducted by the Lead Radius Experiment (PREX) and the Calcium Radius Experiment (CREX) Collaborations have uncovered major deficiencies in the theoretical description of some fundamental properties of atomic nuclei. Following a recent refinement to the isovector sector of covariant energy density functionals we present here additional improvements to the functional by including both tensor couplings and an isoscalar-isovector mixing term in the scalar sector. Motivated by the distinct surface properties of calcium and lead, we expect that the tensor terms that generate derivative couplings will help break the linear correlation between the neutron skin thickness of these two nuclei. Moreover, the addition of these new terms mitigates most of the problems identified by Reed et al. in describing the properties of both finite nuclei and neutron stars. While significant progress has been made in reconciling the PREX-CREX results without compromising other observables, the final resolution awaits the completion of a proper calibration for this new class of functionals. As a result, we expect that powerful reduced basis methods used recently to create efficient emulators will be essential to accomplish this task.

79 ASTRONOMY AND ASTROPHYSICS↗

Pion and kaon parton distribution functions from basis light front quantization and QCD evolution

We investigate the parton distribution functions (PDFs) of the pion and the kaon by combining quantum chromodynamics (QCD) evolution with the basis light front quantization. The initial PDFs result from the light front wave functions obtained by diagonalizing the effective Hamiltonian consisting of the holographic QCD confinement potential, a complementary longitudinal confinement potential, and the color-singlet Nambu–Jona-Lasinio interactions. The valence-quark PDF of the pion, after QCD evolution, is consistent with the result from the E-0615 experiment at Fermilab. Meanwhile, the pion structure function calculated from the PDFs agrees with the ZEUS and the H1 experiments at DESY-HERA for large x. Additionally, the ratio of the up quark PDF of the kaon to that of the pion is in agreement with the NA-003 experiment at CERN. Finally, we also present the cross section for the pion-nucleus induced Drell-Yan process with the obtained pion PDFs supplemented by the PDFs of the target nuclei.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Data-driven predictive probability density function control of fiber length stochastic distribution shaping in refining process

Pulp is the most important raw material in paper in paper industries, whose Fiber Length Stochastic Distribution (FLSD) shaping directly determines the energy consumption and paper quality of the subsequent papermaking processes. However, the mean and variance are insufficient to describe the output FLSD shaping, which display non-Gaussian distribution properties. Therefore, the traditional control, method based on the mean and variance of fiber length is difficult to control the FLSD shaping effectively. In this paper, a novel data-driven predictive probability density function (PDF) control method is proposed for output FLSD shaping in refining process. Primarily, in order to improve the approximation accuracy of the PDF employing RBF neural network, the parameters (center value and width) of each RBF basis functions are tuned via utilizing iterative learning control (ILC) law, and the corresponding estimations of weights law can be obtained. Secondly, considering that the conventional linear model of weights vector has drawbacks of low accuracy and weak generalization ability, random vector functional link networks (RVFLNs) based data driven nonlinear modelling method is employed to characterize the prediction model between the input variables and weights vector. Finally, in order to reduce the randomness of the output FLSD, a minimum entropy control method under mean constraint is employed to design the predictive PDF controller for the output FLSD shaping with the help of the established nonlinear stochastic distribution model. Both simulations and experiments are given to illustrate the effectiveness and practicability of the proposed method.

Probability debsity function, Fiber length distrib↗

RadVolViz: An Information Display-Inspired Transfer Function Editor for Multivariate Volume Visualization

In volume visualization transfer functions are widely used for mapping voxel properties to color and opacity. Typically, volume density data are scalars which require simple 1D transfer functions to achieve this mapping. If the volume densities are vectors of three channels, one can straightforwardly map each channel to either red, green or blue, which requires a trivial extension of the 1D transfer function editor. Here, we devise a new method that applies to volume data with more than three channels. These types of data often arise in scientific scanning applications, where the data are separated into spectral bands or chemical elements. Our method expands on prior work in which a multivariate information display, RadViz, was fused with a radial color map, in order to visualize multi-band 2D images. In this work, we extend this joint interface to blended volume rendering. The information display allows users to recognize the presence and value distribution of the multivariate voxels and the joint volume rendering display visualizes their spatial distribution. We design a set of operators and lenses that allow users to interactively control the mapping of the multivariate voxels to opacity and color. This enables users to isolate or emphasize volumetric structures with desired multivariate properties. Furthermore, it turns out that our method also enables more insightful displays even for RGB data. We demonstrate our method with three datasets obtained from spectral electron microscopy, high energy X-ray scanning, and atmospheric science.

36 MATERIALS SCIENCE↗

Beyond leaf habit: generalities in plant function across 97 tropical dry forest tree species

Leaf habit has been hypothesized to define a linkage between the slow-fast plant economic spectrum and the drought resistance-avoidance trade-off in tropical forests (‘slow-safe vs fast-risky’). However, variation in hydraulic traits as a function of leaf habit has rarely been explored for a large number of species. We sampled leaf and branch functional traits of 97 tropical dry forest tree species from four sites to investigate whether patterns of trait variation varied consistently in relation to leaf habit along the ‘slow-safe vs fast-risky’ trade-off. Leaf habit explained from 0% to 43.69% of individual trait variation. We found that evergreen and semi-deciduous species differed in their location along the multivariate trait ordination when compared to deciduous species. While deciduous species showed consistent trait values, evergreen species trait values varied as a function of the site. Last, trait values varied in relation to the proportion of deciduous species in the plant community. Here We found that leaf habit describes the strategies that define drought avoidance and plant economics in tropical trees. However, leaf habit alone does not explain patterns of trait variation, which suggests quantifying site-specific or species-specific uncertainty in trait variation as the way forward.

59 BASIC BIOLOGICAL SCIENCES↗

An integrated framework of plant form and function: the belowground perspective

Summary Plant trait variation drives plant function, community composition and ecosystem processes. However, our current understanding of trait variation disproportionately relies on aboveground observations. Here we integrate root traits into the global framework of plant form and function. We developed and tested an overarching conceptual framework that integrates two recently identified root trait gradients with a well‐established aboveground plant trait framework. We confronted our novel framework with published relationships between above‐ and belowground trait analogues and with multivariate analyses of above‐ and belowground traits of 2510 species. Our traits represent the leaf and root conservation gradients (specific leaf area, leaf and root nitrogen concentration, and root tissue density), the root collaboration gradient (root diameter and specific root length) and the plant size gradient (plant height and rooting depth). We found that an integrated, whole‐plant trait space required as much as four axes. The two main axes represented the fast–slow ‘conservation’ gradient on which leaf and fine‐root traits were well aligned, and the ‘collaboration’ gradient in roots. The two additional axes were separate, orthogonal plant size axes for height and rooting depth. This perspective on the multidimensional nature of plant trait variation better encompasses plant function and influence on the surrounding environment.

59 BASIC BIOLOGICAL SCIENCES↗

Vapor-phase grafting of functional silanes on atomic layer deposited Al 2 O 3

Fundamental studies are needed to advance our understanding of selective adsorption in aqueous environments and develop more effective sorbents and filters for water treatment. Vapor-phase grafting of functional silanes is an effective method to prepare well-defined surfaces to study selective adsorption. In this investigation, we perform vapor phase grafting of five different silane compounds on aluminum oxide (Al2O3) surfaces prepared by atomic layer deposition. These silane compounds have the general formula L3Si–C3H6–X where the ligand, L, controls the reactivity with the hydroxylated Al2O3 surface and the functional moiety, X, dictates the surface properties of the grafted layer. We study the grafting process using in situ Fourier transform infrared spectroscopy and ex situ x-ray photoelectron spectroscopy measurements, and we characterize the surfaces using scanning electron microscopy, atomic force microscopy, and water contact angle measurements. Here, we found that the structure and density of grafted aminosilanes are influenced by their chemical reactivity and steric constraints around the silicon atom as well as by the nature of the anchoring functional groups. Methyl substituted aminosilanes yielded more hydrophobic surfaces with a higher surface density at higher grafting temperatures. Thiol and nitrile terminated silanes were also studied and compared to the aminosilane terminated surfaces. Uniform monolayer coatings were observed for ethoxy-based silanes, but chlorosilanes exhibited nonuniform coatings as verified by atomic force microscopy measurements.

36 MATERIALS SCIENCE↗

Multiscale Neural Networks for Approximating Green’s Functions

Neural networks (NNs) have been widely used to solve partial differential equations (PDEs) in the applications of physics, biology, and engineering. One effective approach for solving PDEs with a fixed differential operator is learning Green’s functions. However, Green’s functions are notoriously difficult to learn due to their poor regularity, which typically requires larger NNs and longer training times. In this work, we address these challenges by leveraging multiscale NNs to learn Green’s functions. Through theoretical analysis using multiscale Barron space methods and experimental validation, we show that the multiscale approach significantly reduces the necessary NN size and accelerates training.

97 MATHEMATICS AND COMPUTING↗

NGEE Arctic Phase 4 Plant Functional Type Framework for Pan-Arctic Vegetation

The NGEE-Arctic research team identified a common set of hierarchical plant functional types (PFTs) for pan-arctic vegetation that we will use across our research activities. Interdisciplinary work within a large team requires agreement regarding levels of functional organization so that knowledge, data, and technologies can be shared and combined effectively. The team has identified plant functional types as a crucial area where such interoperability is needed. PFTs are used to represent plant pools and fluxes within models, summarize observational data, and map vegetation across the landscape. Within each of these applications, varying levels of PFT specificity are needed according to the specific scientific research goal, computational limitations, and data availability. By agreeing on a specific hierarchical framework for grouping variables in our vegetation data, we ensure the resulting research products will be robust, flexible, and scalable. In this document, we lay out the agreed upon PFT framework with definitions and references to existing literature. Table 1 included in the "NGA700_Phase4PFTFramework_about*" file outlines the relationship between NGEE-Arctic Phase 4, Tier 1 PFTs and the PFTs used within prominent arctic literature as well as publications by the NGEE-Arctic team during phases 1-3.This dataset consists of a table detailing a hierarchical PFT framework that spans 4 tiers with the most granular PFTs listed in tier 1 and the most general PFTs in tier 4. The PFTs within each tier has a single column in the dataset where the PFTs are named and a separate column where the characteristics used to define that PFT are listed. Grey fill of the cells is used to indicate where a given PFT starts to “lose” tier 1 details as you look from left to right. Note the excel file has merged cells to indicate grouping of PFTs across the Tiers- it will not translate into a delimited filetype (.csv, .txt, etc) without modification thus the hierarchical PFT framework table is available in three different file formats: 1) NGA700_Phase4PTS.xlsx – maintains the merged cells and grey fill; 2) NGA700_Phase4PTS.csv – merged cells are split, and grey fill is removed; 3) NGA700_Phase4PTS.pdf – image of the table with merged cells and grey fill. Metadata document included as a *.pdf and file-level metadata and data dictionary as *.csv files.

54 ENVIRONMENTAL SCIENCES↗

Composites of functional polymers: Toward physical intelligence using flexible and soft materials

Abstract Materials that can assist with perception and responsivity of an engineered machine are said to promote physical intelligence. Physical intelligence may be important for flexible and soft materials that will be used in applications like soft robotics, wearable computers, and healthcare. These applications require stimuli responsivity, sensing, and actuation that allow a machine to perceive and react to its environment. The development of materials that exhibit some form of physical intelligence has relied on functional polymers and composites that contain these polymers. This review will focus on composites of functional polymers that display physical intelligence by assisting with perception, responsivity, or by off-loading computation. Composites of liquid crystal elastomers, shape-memory polymers, hydrogels, self-healing materials, and transient materials and their functionalities are examined with a viewpoint that considers physical intelligence. Graphic Abstract

36 MATERIALS SCIENCE↗